Updates

Model and report changes

  1. The model has the ability to incorporate estimates of community prevalence, by region and age group, from the Office of National Statistics COVID-19 Infection Survey (see Data Sources for details). These are included weekly over the last 8 weeks and for the age groups >4 years to inform trends in incidence that are too recent to be captured by the data on deaths. In recent weeks we have been using these data, but do not include them in the analysis here due to the difficulty in resolving conflicting signals coming from the two datasets.
  2. The model now accounts for the ongoing immunisation programme, stratifying the population of people still susceptible to infection with the virus according to their immunisation status (unimmunised/1 dose/2 doses). We use data on the daily proportions of the population getting immunised to inform this splitting of the population, assuming that it takes three weeks for vaccine-derived immunity to develop .
  3. The geographical definition has been changed from the seven NHS regions (map) to the nine regions typically used in government (map). This new spatial definition more appropriately reflects the existing regional heterogeneity.
  4. Using observations of improved survival in hospitalised COVID-19 patients, we have allowed the probability of dying following infection with SARS-CoV2 (the infection-fatality rate, IFR) to gradually change over the course of June 2020, with a decrease being estimated. More recently, the Kent variant of the virus has gradually become the predominant virus strain and we accordingly allow for a change in the IFR over the period in which the relative prevalence of this strain has been growing.
  5. The ‘Epidemic summary’ now only reports the current value for the IFR by age. To visualise how this has changed over time in our model, see the IFR tab in the ‘Infections and Deaths’ section of the report. The quantity that is now plotted under this tab is the probability of dying if infected, taking into account the impact of the immunisation programme.
  6. The modelling now accounts for a different susceptibility to infection in the under-15s, using information from literature (Viner et al, 2020) suggesting that children less likely to acquire infection when in contact with an infectious individual.

Updated findings

  1. The current estimate of the daily number of new infections occurring each day across England is 4,730 (3,390–6,670, 95% credible interval).
  2. The daily infection rate is estimated to be the highest in the West Midlands (WM), East Midlands (EM), Yorkshire and the Humber (YH) and the North East (NE) with 692, 433, 474 and 245 new daily infections, corresponding to 12, 9, 9 and 9 per 100,000 population, respectively. Note these regional estimates are highly uncertain and that a substantial proportion of these daily infections will be asymptomatic.
  3. We predict that the number of deaths occurring daily is likely to remain low with a forecast for the period around the 14th May suggesting that there will be between 21 and 59 deaths per day.
  4. The probability of Rt exceeding 1 is 73%, 68% and 64% in the South West (SW)WM, London (GL) and WM, respectively; 55% and 54% in the in the East of England (EE) and South East (SE); around 30% in Yorkshire and Humber (YH), EM and NE; and approximately 20% in NW. WM is the only region with a higher estimate for both incidence and Rt.
  5. The growth rate for England is estimated to be positive at 0.01 (-0.01–0.03, 95% credible interval) per day. This means that, nationally, the number of infections is increasing, although there is heterogeneity across regions, with negative growth in some of them.
  6. London, followed by the WM and the NE, have the highest attack rates, that is the proportions of the regional populations who have ever been infected, with 33%, 21% and 20% respectively. The SW continues to have the lowest attack rate at 10%. These constitute a big downward revision from our previous published report, particularly so for the NW.
  7. Note that the deaths data used are only very weakly informative on Rt over the last two weeks and are thankfully becoming increasingly sparse. Therefore, the estimate for current incidence, Rt and the forecast of daily numbers of deaths are likely to be subject to some revision.

Interpretation

The plots of the estimated Rt in the most recent weeks are heavily influenced by the effects that the Easter holidays and the gradual relaxation of pandemic mitigation measures have on mobility. Currently, as restrictions are being relaxed we anticipate a very gradually increasing Rt over the coming weeks.. The Rt for five regions have central estimates just above 1 (EE, GL, SE, SW, WM), although these estimates are uncertain. At current levels of incidence, these values of Rt are not a particular concern, though they do require careful monitoring as the national lock-down is gradually relaxed.

The incidence of deaths has continued to fall more sharply than predicted by the model, with a transition to plateau still anticipated. The number of new infections, as the Rt values indicate, is also flat in almost all regions.

The plot of the infection fatality rate (IFR) presents age-specific probabilities of death given infection. It shows an increasing mortality risk from September onwards in all ages until the immunisation programme begins to have an impact in late January. From the end of January we estimate a decreasing IFR in all adult age groups, but most steeply in the older ages. This drop measures the benefits of immunisation against death over and above the benefits against infection. Specifically, there is an estimated fall to a still-high 15%% in the over-75s and 0.5% overall. The overall impact of the immunisation programme can be seen more clearly in the ‘All Ages’ plot, where the precipitous decline in IFR since late January is a product of this efficacy against death but also of the increasing proportion of infections in young people as older age groups are immunised and become protected against infection. The impact of the second immunisation doses becoming widespread will begin to affect this quantity over the coming weeks.

Since the last published report, the estimates of cumulative infection have been revised substantially downwards. This is due to the inclusion of the prevalence data, which have the effect of reducing the number of infections. Nowhere is this more true than in the North West, where estimates of attack rate have fallen from 31% to 18%. London remains the region with the largest levels of cumulative infection to date.

Other indicators (e.g. hospital bed prevalence, reported new cases) continue to suggest a declining epidemic. Prevalence of infection, as estimated by the ONS Community Infections Survey is now around 0.10% in England with some regional heterogeneity. It is hoped that this trend continues as further pandemic measures are progressively relaxed along the government’s roadmap to opening society. We will continue to monitor the situation closely.

Summary

Real-time tracking of an epidemic, as data accumulate over time, is an essential component of a public health response to a new outbreak. A team of statistical modellers at the MRC Biostatistics Unit (BSU), University of Cambridge, are working to provide regular now-casts and forecasts of COVID-19 infections and deaths. This information feeds directly to the SAGE sub-group, Scientific Pandemic Influenza sub-group on Modelling (SPI-M), and to regional Public Health England (PHE) teams.

Methods

We fit a transmission model (Birrell et al. 2020) to a number of data sources (see ‘Data Sources’), to reconstruct the number of new COVID-19 infections over time in different age groups and NHS regions, estimate a measure of ongoing transmission and predict the number of new COVID-19 deaths.

Data sources

We use:

  1. Data on COVID-19 confirmed deaths from the Public Health England (PHE) line-listing This consists of a combination of deaths notified to:
    • the Demographics Batch Service (DBS), a mechanism that allows PHE to submit a file of patient information to the National Health Service spine for tracing against the personal demographics service (PDS). PHE submit a line list of patients diagnosed with COVID-19 to DBS daily. The file is returned with a death flag and date of death updated (started 20th March, 2020).
    • NHS England, who report data from NHS trusts relating to patients who have died after admission to hospital or within emergency department settings.
    • Health Protection Teams (HPTs), resulting from a select survey created by PHE to capture deaths occurring outside of hospital settings, e.g. care homes (started 23rd March, 2020)
  2. Data on antibody prevalence in blood samples from a PHE survey of NHS Blood Transfusion (NHSBT) donors.

Data are stratified into eight age groups: <1, 1-4, 5-14, 15-24, 25-44, 45-64, 65-74, 75+, and the NHS England regions (North East and Yorkshire, North West, Midlands, East of England, London, South East, South West).

  1. Published information on the the natural history of COVID-19 (Verity et al., 2020; Li et al, 2020)
  2. Information on contacts between different age groups from:
    • A Survey that describes relative rates of contacts between different age groups (Mossong et al. 2008).
    • Google Community Mobility reports, informing the changes in people’s mobility over the course of the pandemic, particularly after the March 23rd lockdown measures.
    • The ONS’ time use survey, which in conjunction with the google mobility study, allows estimation of the changing exposure to infection risk over time.
    • Data from the Department for Education describing the proportion of children currently attending school.
  3. Daily data on the numbers of people getting immunised by age-group and region. These data are derived from the National Immunisation Management Service (NIMS). These data includes all COVID-19 immunisations administered at hospital hubs, local immunisation service sites such as GP practices, and dedicated immunisation centres.

Epidemic summary

Current \(R_t\)

Value of \(R_t\), the average number of secondary infections due to a typical infection today.

Number of infections

Attack rate

The percentage of a given group that has been infected.

By region

By age

Current IFR

Change in infections incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England 0.01 -0.01 0.03
East of England 0.00 -0.04 0.04
East Midlands -0.01 -0.05 0.02
London 0.01 -0.03 0.04
North East -0.01 -0.05 0.03
North West -0.01 -0.05 0.01
South East 0.00 -0.04 0.03
South West 0.01 -0.03 0.05
West Midlands 0.01 -0.03 0.04
Yorkshire and The Humber -0.01 -0.05 0.03

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA 111.85 NA
East of England NA 16.06 NA
East Midlands 70.24 14.08 NA
London NA 22.85 NA
North East 79.28 13.51 NA
North West 46.77 13.83 NA
South East NA 18.05 NA
South West NA 27.00 NA
West Midlands NA 23.04 NA
Yorkshire and The Humber 87.87 13.54 NA

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 86.06 27.33 NA
East of England 522.06 16.98 NA
East Midlands NA 27.73 NA
London 100.34 17.15 NA
North East NA 26.72 NA
North West NA 48.80 NA
South East 586.44 20.83 NA
South West 58.02 14.26 NA
West Midlands 88.88 17.17 NA
Yorkshire and The Humber NA 24.09 NA

Change in deaths incidence

Growth rates

NB: negative growth rates are rates of decline. Values are daily changes.

Region Median 95% CrI (lower) 95% CrI (upper)
England -0.02 -0.03 -0.01
East of England -0.02 -0.04 0.02
East Midlands -0.03 -0.05 0.00
London -0.01 -0.04 0.01
North East -0.03 -0.05 0.00
North West -0.03 -0.05 0.00
South East -0.02 -0.04 0.01
South West -0.01 -0.04 0.02
West Midlands -0.01 -0.04 0.02
Yorkshire and The Humber -0.02 -0.05 0.00

Halving times

Halving times in days, if a region shows growth than value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England 38.94 25.85 90.35
East of England 42.16 15.56 NA
East Midlands 27.26 14.31 NA
London 50.82 18.03 NA
North East 25.92 13.61 NA
North West 23.92 13.91 147.95
South East 35.55 16.05 NA
South West 81.04 18.69 NA
West Midlands 46.60 17.11 NA
Yorkshire and The Humber 27.45 14.28 NA

Doubling times

Doubling times in days, if a region shows decline then the value will be NA.

Region Median 95% CrI (lower) 95% CrI (upper)
England NA NA NA
East of England NA 44.86 NA
East Midlands NA 196.51 NA
London NA 46.26 NA
North East NA 209.60 NA
North West NA NA NA
South East NA 85.20 NA
South West NA 28.59 NA
West Midlands NA 42.86 NA
Yorkshire and The Humber NA 240.98 NA

Infections and deaths

The shaded areas show periods of national lockdown, the green lines the dates (once confirmed) of the steps in the roadmap in the UK Governement’s COVID-19 Response – Spring 2021, and the red line shows the date these results were produced (23 Apr).

Infection incidence

By region

By age

Cumulative infections

By region

By age

Deaths incidence

By region

By age

Cumulative deaths

By region

By age

IFR

Prob \(R_t > 1\)

The figure below shows the probability that \(R_t\) is greater than 1 (ie: the number of infections is growing) in each region over time. Clicking the regions in the legend allows lines to be added or removed from the figure.

\(R_t\)

Copyright © MRC Biostatistics Unit, University of Cambridge